Mass Effect: Athena
by scarface101
Summary: What if it wasn't Cerberus that saved Commander Shepherd? What if it was someone, something else? Paragon (M) Shepxharem.


**A/N. I just finished the Mass Effect Trilogy, and I was somewhat disappointed with how No. 3 ended. Good game, but the ending was… depressing. So this idea has been in my head since I finished the Trilogy. It will feature a Paragon male Shepard, with a small harem of three to five girls. Not a lot of Shepard x harem stories, but c'mon! He's saving the entire damn galaxy! I think he deserves it. Thus far the only confirmed girls are Liara and Tali, but by all means put in your suggestions. And please forgive me about the inaccuracy of the dialogue and spelling mistakes, this story won't entirely follow canon. Thank you and enjoy!**

**This fan-fic was brought to you by Scarface101 and Kid Buu 619.**

**Disclaimer: We don't own Mass Effect.**

**Chapter one: Missing in action.**

Gone. That was the only word that could be said. The Normandy was gone. Destroyed by the mysterious ship that came out of nowhere. It had been five days since that brutal attack. Most of the crew escaped with their lives, Navigator Presly and a few others didn't, as for Commander Jack Shepherd, it hasn't been confirmed whether he was alive or dead. Which made one Liara T'soni pace restlessly across the bridge of the ship lent to them by Admiral Hackett.

Garrus Vakarian, felt sorry for his Asari crewmate, after all it was Shepherd that helped him realize that being in C-sec didn't just mean arresting criminals it also meant protecting Civilians. His mandibles twitched a bit until he finally said "Take it easy Liara, we'll find Shepherd. He's a tough bastard, he'll pull through." The former archeologist nodded and stopped pacing in an attempt to calm her nerves, she tried taking deep slow breaths, it worked for a moment but her worried state refused to disappear so she resumed pacing. The Turian sniper sighed in defeat and just chose to remain silent for the rest of the flight.

After a few more minutes the other crewmates appeared: Kaiden Alenko, Tali Zorah, and Urdnot Wrex. Kaiden was tapping on his helmet nervously, Tali's face couldn't be seen clearly through her enviro-suits helmet, but you could tell by her body language she was worried, and Wrex was crossing his arms while occasionally grunting, in frustration at the wait. Joker spoke through the loudspeaker saying "We're almost there; let's hope we're not too late."

They arrived at their destination, the wreckage of the SSV Normandy. It was a sad sight to see the ship they served on smashed into pieces like this, but they were here to find their leader, and more importantly, their friend: Shepherd.

The five squad-mates each took a shuttle to search the wreckage for their friend. After hours of searching, they couldn't find a trace of their friend. The situation was looking hopeless, and the Asari felt like her heart was breaking apart, at the fact she lost her bond-mate so quickly. However a radio transmission from Tali broke the crew's silence, the Quarian engineer said "Everyone! I found something!" the shuttles quickly turned to investigate Tali's finding. It was a beacon, with Shepherd's dog tags tied to it.

They all agreed that the beacon was the only clue they had so they brought it aboard the SSV Hamilton. After waiting for Joker to join them it activated revealing a Holo recording of what was obviously a very advanced mech that appeared to be female **(A/N. It looks like EDI in ME3, and EDI won't appear in this story. I like her, but this is necessary.)**

The Hologram spoke with a small smile "Greetings to you. I would introduce myself but I have no name. I am Commander Shepherd's savior. Do not worry, he is alive and well, but I'm afraid I need to 'borrow' him for an unknown amount of time; but do know that he will need all of you again when the Reaper threat returns. Until then, train yourselves and improve your skills, for you will need every single ounce of skill and courage to survive the coming storm. Goodbye and I hope we soon meet in person."

The hologram disappeared leaving some very confused individuals. Inside Liara was happy that her bond-mate was still alive, but she and her crewmates were now even more confused, because they now had even more questions and not enough answers.

**Somewhere in the Far Rim.**

Commander Shepherd was asleep on a medi-bay bed, completely oblivious to his surroundings, until his eyes fluttered open. He looked around, and took notice of the room. It was sterile white just like any other hospital he visited, but next to him were his armor and weapons, and by looks of it they had been cleaned and modified. He heard the door open and quickly shut his eyes to pretend he was still asleep.

The unknown person said "The Commander still appears to be unconscious, I shall continue to moniter." Shepherd heard the approaching footsteps and got ready to attack his captor, he felt his captor touch his arm and said "Ah, it seems the Commander has attempted to feign sleep." The Commander snapped his eyes open saw a strange alien he had never seen before in his life.

The Alien said "Calm yourself Commander, I am an ally." Shepherd relaxed slightly but didn't let his guard down, he then asked "Who are you? And what species are you?" the Alien answered "My name is Javik, and I am a Prothean." The Commander was in disbelief and retorted "You can't be a Prothean; they all died fifty-thousand year's ago." Javik nodded and said "True, but I assure you I AM a Prothean; I was trapped in suspended animation since the previous Reaper Invasion, but I was woken up, by an… unexpected ally."

The Commander raised an eyebrow and said more calmly "Okay, but who woke you up?" the Prothean replied "It would be better if you meet her for yourself. Come I will show you to her." Shepherd nodded and followed the Prothean down several hallways until they entered what appeared to be a bridge. Javik exited the room, while Shepherd walked towards a feminine silhouette. The figure turned revealing a mech that was made to look like a woman, she smiled and said "Greetings to you Commander, I'd give you my name, but I do not have one."

Shepherd, looked curiously at the mech and asked "What are you? An AI installed inside a mech?" the mech seemed to hesitate as if she was considering her answer, finally she replied "I am a Reaper." This instantly got Shepherd on guard, she then said "Let me explain…" she was interrupted by the Commander interrupted her saying "What so you can indoctrinate me?" she shook her head saying "No, please hear me out Commander, if you are dissatisfied with my explanation then I shall gladly drop you off at the Citadel. No strings attached." The Commander thought for a moment, after a few moments he nodded, it couldn't hurt to listen, right?

He nodded, causing the now revealed Reaper to explain "Many millennia ago, we the Reapers were created to protect and preserve all organic life, I was the first, the most powerful, and I was given the ability of choice. However, the creator's made a program to continue their work, even after they disappeared; the program evolved and decided to 'preserve' organic life by obliterating the more evolved species, allowing the younger ones to 'grow', ironically the first species to be harvested was the Creator's themselves. I attempted to destroy the program, but it had already created many 'Reapers' before my retaliation, and I was quickly defeated, but not destroyed. I retreated into dark space, and decided to go into hibernation, in my 'sleep' I plotted and planned on how to destroy the program. I decided to try and talk to find a way to negotiate with you organics, hence why I created this mech in order to better interact with you. I have watched and observed since, the Reaper you refer to as 'Sovereign' invaded, and you have impressed me, I believe you are the only one capable of leading an Army to destroy the rogue program."

The Commander was shocked at her explanation, and said "If what you say is true, then you know first-hand what's coming, and I'll either need an army or a good team." The Reaper raised a metallic eyebrow and said "I'm surprised that you are so readily accepting a partnership with me." Shepherd replied "You could have lied to me, and I have no real reason not to believe you, but you must earn my trust. Until then cooperation will be needed."

The Reaper nodded and said "Excellent, then it will be easier to show you I'm on your side. Now please rest. I shall alert you when we arrive at our destination." "And what is our destination?" the Commander asked; the Reaper replied "Akuze, that is where my main base is. It is there I shall help prepare you for the coming invasion; before you leave for your quarters, I must ask you to imprint your DNA into this panel so that I will obey your orders without question." A panel appeared from the floor with the shape of a hand on the holo board.

Shepherd placed his hand on the board, it flashed green, confirming that his DNA was registered. The Commander turned to the Reaper mech and asked "What is your name?" the Reaper replied "As I said before, I don't have one. Since you are now in command of me, then you must give me a name."

The Commander thought for a moment and said "I shall call you Athena." The Reaper said "Athena; the Greek goddess. Representative of Wisdom, Law and Justice, and Just Warfare. An appropriate name; I accept the name 'Athena.'"

The Commander nodded and was guided to his quarters by a VI drone. Once he arrived at his quarters he was stunned to see the wide assortment of armor and weapons making him think _'Is this the captain's cabin or the armory?'_ he sighed and headed towards the bed, his thoughts went out to his crew, including Liara. He sighed again and fell asleep while wondering how he was going to explain to his crew about Athena.

Meanwhile Athena smiled to herself and said "Excellent, now I must compile a list of possible recruits and for his crew, and start on creating his own private army."

**Chapter one End.**

**A/N. Yes I know, this chapter was rushed, but please review and give me your thoughts, Happy Valentines to you! Thank you and may God bless America.**


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